Agricultural Science Digest

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Research Article

Agricultural Science Digest, volume 37 issue 3 (september 2017) : 185-190

In silico analysis, structural modeling and phylogenetic analysis of EPSP synthase of Phaseolus vulgaris 
 

Meenu Goyal, Sugandh Chauhan, Pardeep Kumar
1Department of Biotechnology, Central University of Haryana, Mahendergarh 123 031, Haryana, India.
Cite article:- Goyal Meenu, Chauhan Sugandh, Kumar Pardeep (2017). In silico analysis, structural modeling and phylogenetic analysis of EPSP synthase of Phaseolus vulgaris. Agricultural Science Digest. 37(3): 185-190. doi: 10.18805/asd.v37i03.8986.

ABSTRACT

The 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase is one of the essential enzymes of shikimate pathway and is verified as a specific target of broad-spectrum herbicide glyphosate. It is important to get insights into three-dimensional (3D) structure of this enzyme for engineering new herbicides as well as herbicide resistant crops. The information about 3D structure of EPSP synthase enzyme is not yet available in protein database for any of the plant species. Therefore, we revealed the homology model of Phaseolus vulgaris EPSP synthase protein using the structure of EPSP synthase from E. coli as template. The resulting model structure was refined by RAMPAGE server, ERRAT and Verify3D. Ramachandran plot analysis showed that conformations for 95.6% of amino acid residues are within the most favoured region. The phylogenetic tree (constructed using MAFFT) separated EPSP synthases of bacteria, monocot and dicot plants into distinct clusters. Our study generated reliable 3D model structure of EPSP synthase in P. vulgaris, which can be used for future studies.

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